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SystemVerilog Framework for DMA Controllers Verification
Zachariášová, Marcela ; Martínek, Tomáš (referee) ; Puš, Viktor (advisor)
In contemporary hardware design, verification techniques are exploited to verify the function of hardware components as well as complex systems. This thesis deals with functional verification of DMA controllers. It describes the theoretical principles of verification using the SystemVerilog language and the principles of DMA data transfer. The design of controllers is described, with the focus on design of the verification environment and results of the verification.
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Hardware Accelerating of Encryption Algorithm
Hradil, David ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
The goal of this thesis is to design a hardware realization of circuit which will implement the AES algorithm. A motivation was to make an acceleration against the classic software encryption. The acceleration is achieved by special designed parts of the circuit, which correspond to particular operations of the AES algorithm. First, there was necessary to design the circuit. In the next step there was a need to describe the designed circuit by the VHDL language. Then the circuit was simulated and synthesized. Due to comparing the circuit with software processing a software implementation was created. Both implementations were created for the FITKit platform. The hardware implementation is made by the FPGA technology and the software implementation is realized in a microcontroller. The result of the thesis is almost one thousandfold acceleration against the classic software encryption.
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Analysis of DNA Structure Elements
Knytl, Marek ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The aim of this master's thesis is the design and implementation of tool trackAnalysis for statistical analysis of DNA structure elements. The positions of individual elements in genome are obtained in the form of the track, and with these positions the tool performs a set of analyzes, including randomness test of track, test examining distances between track and genes, detection of clusters and overlaps. The indivudual tests results can be linked together. The results will be displayed in the form of a list, a graph or a new annotation track. An important part of this thesis is also testing the resulting tool on a set of real data.
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Implementation of Encryption Algorithms in VHDL Language
Kožený, Petr ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
This thesis deals with design and implementation of AES and DES encryption architectures for embedded systems. Architectures are implemented in VHDL language and design for FPGA technology. The proposed implementations are mapped on the Xilinx Spartan 3 technology. Both architectures are applied in simple ECB (Electronic Codebook) scheme with cache memories. A maximum throughput of design DES architecture 370 Mbps is achived with clock frequency of 104 MHz. The throughput of AES architecture at the maximum clock frequency of 118 MHz is 228 Mbps. Compared to software implementations for embedded systems, we achieve significantly higher throughput for both architectures.
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System of Internal Buses for Chips with FPGA Technology
Málek, Tomáš ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
This thesis deals with design and implementation of interconnection bus system for chips with FPGA technology. The system ensures both communication between internal components on a chip and their communication with other computer elements which are mapped to the host system memory. The buses are high-speed, full duplex and packet-oriented and their architecture is based on tree topology. The data width is configurable, individually for every bus part. Due to this feature, it is possible to build uniform hierarchical system of internal buses with different speed that interconnects differently fast components. Proposed interconnection system was implemented in VHDL language and it is utilized in the Liberouter project which is the part of CESNET research intention Programable Hardware.
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Processing and Visualization of Mass Spectrums
Beneš, Ondřej ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
One of new techniques in the field of analytical chemistry, which has more and more practical use, is mass spectrometry imaging. With its ability to record representation of substances in samples during the tissue analyze arise problem with a lot of output data which needs to be handled programmatically. The goal of this work is to create an software for processing and visualization data of new standard imzML. As a part of the work, the field of mass spectrometry, primarily MALDI TOF mass spectrometry, is briefly introduced. There are also introduced some methods for mass spectrometry data preprocessing. The work also contains a summary of current state of available software for processing and visualization of mass spectrometry data. With requests from cooperating laboratory a novel software is designed and implemented, which besides the visualization itself, can preprocess the data for example data smoothing with Savitzky-Golay method, internal calibration or peak detection with continuous wavelet transformation. The software was successfully tested on real data sets.
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Time Synchronization in Computer Networks
Matoušek, Denis ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
The master's thesis deals with design of a solution for time synchronization in computer networks that is a crucial problem of many network applications. Based on analysis of protocols for time synchronization, PTP protocol was chosen as an appropriate candidate. The thesis describes the implementation of the design for a special network interface card and demonstrates features of the solution in several tests. A part of the solution processing precise timestamps was implemented in FPGA chip on the network card while PTP messages are processed in a software application. Values of configurable parameters of the application were determined based on analysis of the network card properties and results of particular tests. It was achieved accuracy in order of tens of nanoseconds.
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Fast Processing of Application-Layer Protocols
Bárta, Stanislav ; Martínek, Tomáš (referee) ; Polčák, Libor (advisor)
This master's thesis describes the design and implementation of system for processing application protocols in high-speed networks using the concept of Software Defined Monitoring. The proposed solution benefits from hardware accelerated network card performing pre-processing of network traffic based on the feedback from monitoring applications. The proposed system performs pre-processing and filtering of network traffic which is handed afterwards passed to application modules. Application modules process application protocols and generate metadata that describe network traffic. Pre-processing consists of parsing of network protocols up to the transport layer, TCP reassembling and forwarding packet flow only to modules that are looking for a given network traffic. The proposed system closely links intercept related information internal interception function (IRI-IIF) and content of communication internal interception function (CC-IIF) to minimize the performing of duplicate operations and increase the efficiency of the system.
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MiWi Protocol Driver for Linux
Wolfert, Richard ; Martínek, Tomáš (referee) ; Novotný, Tomáš (advisor)
This bachelor's thesis describes creating of device driver for Linux. The result driver is able to handle PAN coordinator device for MiWi protocol. User is able to communicate with device using socket network interface. The theoretical part provides fundamentals of operations and creation of new device drivers for Linux kernel. The main parts of this work consist of design, implementation, final testing and evaluation of results
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Predictor of the Effect of Amino Acid Substitutions on Protein Function
Musil, Miloš ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This thesis discusses the issue of predicting of the effect of amino acid substitutions on protein funkcion, based on phylogenetic analysis method, inspired by tool MAPP. Significant number of genetic diseases is caused by nonsynonymous SNPs manifested as single point mutations on the protein level. The ability to identify deleterious substitutions could be useful for protein engineering to test whether the proposed mutations do not damage protein function same as for targeting disease causing harmful mutations. However the experimental validation is costly and the need of predictive computation methods has risen. This thesis describes desing and implementation of a new in silico predictor based on the principles of evolutionary analysis and dissimilarity between original and substituting amino acid physico-chemical properties. Developed algorithm was tested on four datasets with 74,192 mutations from 16,256 sequences in total. The predictor yields up to 72 % accuracy and in the comparison with the most existing tools, it is substantially less time consuming. In order to achieve the highest possible efficiency, the optimization process was focused on selection of the most suitable (a) third-party software for calculation of a multiple sequence alignment, (b) overall decision threshold and (c) a set of physico-chemical properties.
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